Genomic and pedigree estimation of inbreeding depression for semen traits in the Basco-Béarnaise dairy sheep breed.

Autor:	Antonios S; GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France., Rodríguez-Ramilo ST; GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France., Aguilar I; Instituto Nacional de Investigación Agropecuaria (INIA), 11100, Montevideo, Uruguay., Astruc JM; Institut de l'Elevage, 149 rue de Bercy, F-75595 Paris, France., Legarra A; GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France., Vitezica ZG; GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France. Electronic address: zulma.vitezica@inrae.fr.
Jazyk:	angličtina
Zdroj:	Journal of dairy science [J Dairy Sci] 2021 Mar; Vol. 104 (3), pp. 3221-3230. Date of Electronic Publication: 2020 Dec 25.
DOI:	10.3168/jds.2020-18761
Abstrakt:	Inbreeding depression is associated with a decrease in performance and fitness of the animals. The goal of this study was to evaluate pedigree-based and genomic methods to estimate the level of inbreeding and inbreeding depression for 3 semen traits (volume, concentration, and motility score) in the Basco-Béarnaise sheep breed. Data comprised 16,196 (or 15,071) phenotypic records from 620 rams (of which 533 rams had genotypes of 36,464 SNPs). The pedigree included 8,266 animals, composed of the 620 rams and their ancestors. The number of equivalent complete generations for the 620 rams was 7.04. Inbreeding coefficients were estimated using genomic and pedigree-based information. Genomic inbreeding coefficients were estimated from individual SNP and using segments of homozygous SNP (runs of homozygosity, ROH). Short ROH are of old origin, whereas long ROH are due to recent inbreeding. Considering that the equivalent number of generations in Basco-Béarnaise was 6, inbreeding coefficients for ROH with a length >4 Mb refer to all (recent + old) inbreeding, those with a length >17 Mb correspond to recent inbreeding, and the difference between them indicates old inbreeding. Pedigree-based inbreeding coefficients were also estimated classically, or accounting for nonzero relationships for unknown parents, or including metafounder relationships (estimated using markers) to account for missing pedigree information. Finally, inbreeding coefficients combining genotyped and nongenotyped animal information were computed from matrix H of the single-step approach, also including metafounders. Inbreeding depression was estimated differently depending on the approach used to compute inbreeding coefficients. These 8 estimators of inbreeding coefficients were included as covariates in different animal models. No inbreeding depression was detected for sperm volume or sperm concentration. Inbreeding depression was significant for the motility of spermatozoa. The effect of old and recent inbreeding on motility was null and negative, respectively, demonstrating the existence of purging by selection of deleterious recessive alleles affecting motility. A 10% increase in inbreeding would result in a reduction in mean motility ranging between 0.09 and 0.22 points in the score (from 0 to 5). Motility is unfavorably affected by increasing recent inbreeding but the impact is very small. Runs of homozygosity and metafounders allow us to accurately estimate inbreeding depression and detect recent inbreeding. (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)
Databáze:	MEDLINE
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